Housing allowance must be approved by the governing body of your church before it is paid to you. It is my understanding that it cannot be approved retroactively. A minister cannot self-declare that income is housing allowance. It must be designated as such by the church and properly recorded in the minutes that allocated it and properly indicated in each paycheck.
Without such a paper trail all the income paid by the church is considered income not designated housing allowance.
I'll reiterate, as I always do, that I am not an accountant.
I highly recommend you and the religious organization consult an accountant in this particular situation. It is never too late to request a W-2 or 1099, if one should have been issued.
I have also heard that it is a crime for a treasurer not to issue w-2s and 1099s if they should have been issued. So again please be careful and consult a professional.
